Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 5421 |
| PDBID: | 7WP5 |
| Chains: | HL_F |
| Organism: | Homo sapiens, Severe acute respiratory syndrome coronavirus 2 |
| Method: | EM |
| Resolution (Å): | 3.90 |
| Reference: | 10.1038/s41422-022-00638-6 |
| Antibody | |
| Antibody: | VacW-209 Fab |
| Antibody mutation: | No |
| INN (Clinical Trial): | |
| Antigen | |
| Antigen: | SARS-CoV-2 Omicron S6P spike glycoprotein RBD |
| Antigen mutation: | Yes |
| Durg Target: | P0DTC2 |
Sequence information
Antibody
Heavy Chain: H
Mutation: NULL
| >7WP5_H|Chain B[auth H]|VacW-209 heavy chain|Homo sapiens (9606) QVQLVESGGGVVQPGRSLRLSCAASGFTFSSIAMHWVRQAPGKGLEWVAVMSFDGSIKYYGDSVKGRFTISRDNSKSTLYLQMNSLRAEDTAVYYCARGVQGYYDRSGYYNLDYNYGMDVWGQGTTVTVSS |
Light Chain: L
Mutation: NULL
| >7WP5_L|Chain A[auth L]|VacW-209 light chain|Homo sapiens (9606) QSVLTQPPSVSGAPGQRVTISCTGSSSNIGAGYDVHWYQQLPGTAPKLLIYGNSNRPSGVPDRFSGSKSGTSASLAITGLQAEDEADYYCQSYDSSLSGWVFGGGTKLTVL |
Antigen
Chain: F
Mutation: R14K/E152K/N169Y
| >7WP5_F|Chain C[auth F]|Spikeprotein S1|Severe acute respiratory syndrome coronavirus 2 (2697049) TNLCPFDEVFNATRFASVYAWNRKRISNCVADYSVLYNLAPFFTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGNIADYNYKLPDDFTGCVIAWNSNKLDSKVSGNYNYLYRLFRKSNLKPFERDISTEIYQAGNKPCNGVAGFNCYFPLRSYSFRPTYGVGHQPYRVVVLSFELLHAP |
Interaction
1、Solvent accessible surface areas (SASA) were calculated (Naccess V2.1.1) for each residue in antibody and antigen, respectively. The residues with SASA loss in binding of more than 1Å2 were classified as interacting residues.
Interacting residues (ΔSASA based)
| L: ASP34 TYR51 GLY52 ASN53 SER54 ASN55 ARG56 PRO57 SER58 ASP62 SER67 LYS68 H: THR28 ILE32 ARG98 VAL100 GLN101 GLY102 TYR103 TYR104 ASP105 ARG106 SER107 GLY108 ASP113 ASN115 TYR116 ASP119 F: TYR369 ASN370 LEU371 ALA372 PRO373 PHE375 PHE377 LYS378 CYS379 TYR380 GLY381 VAL382 SER383 PRO384 THR385 ASP405 GLU406 ARG408 GLN409 ALA411 PRO412 GLY413 GLN414 THR415 GLY416 ASN417 ASP420 ASP427 ASP428 LEU455 PHE456 HIS505 |
2、We defined interacting paratope-epitope residues by a distance cutoff of < 5Å . Two amino acids are considered as interacting residues if they have at least one atom within a distance of 5 Å from any atom.
Interacting residues (Atom distance based)
